Kroos has been an unused substitute for Bayern's last two matches after reacting angrily to being substituted against Stuttgart two weeks ago.
Lahm admitted that he felt sorry for Kroos but said that his team-mate must respect the wishes of coach Pep Guardiola.
"It's not nice for Toni, that much is clear," Lahm said.
"But the coach makes the decisions and everyone has to accept them."
Germany international Kroos has 18 months left on his current deal, with Manchester United boss David Moyes a known admirer having scouted him earlier this season.
Kroos, who has been capped 41 times by Germany, is said to have already turned down one offer of a contract extension from the Bavarian club.
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